Metabolomics is an omics methodology for the analysis of low-molecular-weight compounds and useful to gain information on the biological effect of medicinal agents. However, in the field of metabolomics, few methods have been established to simultaneously analyze exogenous and endogenous metabolites, which can provide insight into the pharmacological effects and potential mechanisms of action. Sulfur-containing compounds are characteristic constituents of Allium species including garlic, and possess a variety of beneficial effects on health. We have developed a comprehensive analytical method to identify major sulfur-containing compounds and their possible metabolites as well as various endogenous metabolites in plasma. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of 166 reference substances including some sulfur-containing compounds provided information on retention time, accurate mass, and MS/MS parameters. The analytes spiked in rat plasma samples were successfully assigned using metabolite library that were constructed from the acquired reference information and publicly available databases. Subsequently, this method was used to examine the metabolic changes in rat plasma after administration of aged garlic extract (AGE). Immediately after administration of AGE, some sulfur-containing compounds derived from AGE were present at high concentrations in plasma. In addition, AGE administration induced temporal changes of plasma metabolites in rat. These results suggest that our method is useful in capturing changes in sulfur compounds and endogenous metabolites in body fluids associated with the dietary intake of garlic products and may provide a basis for understanding their pharmacological actions.